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Yorodumi- PDB-3kd5: Closed ternary complex of an RB69 gp43 fingers domain mutant comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kd5 | ||||||
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Title | Closed ternary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair and phosphonoformic acid. | ||||||
Components |
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Keywords | TRANSFERASE/DNA / polymerase / gp43 / human cytomegalovirus / hcmv / acyclic guanosine / acyclovir / phosphonoformic acid / foscarnet / foscavir / antiviral / DNA replication / DNA-binding / DNA-directed DNA polymerase / Exonuclease / Hydrolase / Nuclease / Nucleotidyltransferase / Transferase / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage RB69 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / isomorphous replacement / Resolution: 2.69 Å | ||||||
Authors | Zahn, K.E. / Doublie, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Phosphonoformic acid inhibits viral replication by trapping the closed form of the DNA polymerase. Authors: Zahn, K.E. / Tchesnokov, E.P. / Gotte, M. / Doublie, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kd5.cif.gz | 217.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kd5.ent.gz | 168.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kd5_validation.pdf.gz | 465 KB | Display | wwPDB validaton report |
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Full document | 3kd5_full_validation.pdf.gz | 472.2 KB | Display | |
Data in XML | 3kd5_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 3kd5_validation.cif.gz | 50.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/3kd5 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/3kd5 | HTTPS FTP |
-Related structure data
Related structure data | 3kd1SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules TP
#1: DNA chain | Mass: 5492.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide was chemically synthesized. |
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#2: DNA chain | Mass: 4278.780 Da / Num. of mol.: 1 / Fragment: Acyclic GMP terminated primer DNA / Source method: obtained synthetically / Details: Oligonucleotide was chemically synthesized. |
-Protein , 1 types, 1 molecules E
#3: Protein | Mass: 105806.359 Da / Num. of mol.: 1 Fragment: RB69 gp43 exo- chimera containing elements from the fingers domain of the human cytomegalovirus DNA polymerase. Mutation: D222A V478W F479V N480S I557M N558A R559L L561V I562T I563C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43, RB69 gp43 / Plasmid: pPR-IBA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q38087, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 250 molecules
#4: Chemical | ChemComp-PPF / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5% PEG 20000, 0.1M sodium acetate pH5, 0.1M magnesium acetate, 0.1M Tris HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03315 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 2009 Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geomet ry |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03315 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 36065 / Num. obs: 36065 / % possible obs: 100 % / Redundancy: 23.4 % / Biso Wilson estimate: 86.5 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 21.1 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3545 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous replacement Starting model: PDB entry 3KD1 Resolution: 2.69→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 25.02 / SU ML: 0.32 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.787 Å2
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Refinement step | Cycle: LAST / Resolution: 2.69→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.686→2.755 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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